Clostridioides difficile in Latin America: A comprehensive review of literature (1984-2021).

This narrative review summarizes literature on C. difficile and C. difficile infections (CDI) that emerged from Latin America (LA) between 1984 and 2021. The revised information includes papers in English, Spanish, or Portuguese that were retrieved from the databases Pubmed, Scopus, Web of Science, Google Scholar, Scielo, and Lilacs. Information is presented chronologically and segregated in subregions, focusing on clinical presentation, risk factors, detection and typing methods, prevalence and incidence rates, circulating strains, and, when available, phenotypic traits, such as antimicrobial susceptibility patterns. Studies dealing with cases, clinical aspects of CDI, and performance evaluations of diagnostic methods predominated. However, they showed substantial differences in case definitions, measuring units, populations, and experimental designs. Although a handful of autochthonous strains were identified, predominantly in Brazil and Costa Rica, the presentation and epidemiology of CDI in LA were highly comparable to what has been reported in other regions of the world. Few laboratories isolate and type this bacterium and even less generate whole genome sequences or perform basic science on C. difficile. Less than ten countries lead academic productivity on C. difficile or CDI-related topics, and information from various countries in Central America and the Caribbean is still lacking. The review ends with a global interpretation of the data and recommendations to further develop and consolidate this discipline in LA.

Porphyromonas spp. have an extensive host range in ill and healthy individuals and an unexpected environmental distribution: A systematic review and meta-analysis.

Studies on the anaerobic bacteria Porphyromonas, mainly focused on P. gingivalis, have revealed new bacterial structures, metabolic pathways, and physiologic functionalities. Porphyromonas are mainly described as being associated with mammals and involved in chronic oral infections and secondary pathologies such as cancers or neurodegenerative diseases. In this review, we collected and analyzed information regarding Porphyromonas isolation sites and associated conditions and showed that Porphyromonas are detected in numerous pristine and anthropic environments and that their host range appears wider than previously believed, including aquatic animals, arthropods, and birds, even if their predominant hosts remain humans, pets, and farm animals. Our analyses also revealed their presence in multiple organs and in a substantial proportion of healthy contexts. Overall, the growing numbers of microbiota studies have allowed unprecedented advances in the understanding of Porphyromonas ecology but raise questions regarding their phylogenic assignment. In conclusion, this systematic and meta-analysis provides an overview of current knowledge regarding Porphyromonas ecological distribution and encourages additional research to fill the knowledge gaps to better understand their environmental distribution and inter- and intra-species transmission.

Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.

BACKGROUND: Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes are only working drafts, an incompleteness that causes numerous problems and constitutes a major obstacle to genotypic and phenotypic interpretation. In this work, we began with an example from the class Bacteroidia in the phylum Bacteroidetes, which is preponderant among human orodigestive microbiota. We successfully identify the genetic loci responsible for assembly breaks and misassemblies and demonstrate the importance and usefulness of long-read sequencing and curated reannotation. RESULTS: We showed that the fragmentation in Bacteroidia draft genomes assembled from massively parallel sequencing linearly correlates with genomic repeats of the same or greater size than the reads. We also demonstrated that some of these repeats, especially the long ones, correspond to misassembled loci in three reference Porphyromonas gingivalis genomes marked as circularized (thus complete or finished). We prove that even at modest coverage (30X), long-read resequencing together with PCR contiguity verification (rrn operons and an integrative and conjugative element or ICE) can be used to identify and correct the wrongly combined or assembled regions. Finally, although time-consuming and labor-intensive, consistent manual biocuration of three P. gingivalis strains allowed us to compare and correct the existing genomic annotations, resulting in a more accurate interpretation of the genomic differences among these strains. CONCLUSIONS: In this study, we demonstrate the usefulness and importance of long-read sequencing in verifying published genomes (even when complete) and generating assemblies for new bacterial strains/species with high genomic plasticity. We also show that when combined with biological validation processes and diligent biocurated annotation, this strategy helps reduce the propagation of errors in shared databases, thus limiting false conclusions based on incomplete or misleading information.

A Clostridium difficile Lineage Endemic to Costa Rican Hospitals Is Multidrug Resistant by Acquisition of Chromosomal Mutations and Novel Mobile Genetic Elements.

The antimicrobial resistance (AMR) rates and levels recorded for Clostridium difficile are on the rise. This study reports the nature, levels, diversity, and genomic context of the antimicrobial resistance of human C. difficile isolates of the NAPCR1/RT012/ST54 genotype, which caused an outbreak in 2009 and is endemic in Costa Rican hospitals. To this end, we determined the susceptibilities of 38 NAPCR1 isolates to 10 antibiotics from seven classes using Etests or macrodilution tests and examined 31 NAPCR1 whole-genome sequences to identify single nucleotide polymorphisms (SNPs) and genes that could explain the resistance phenotypes observed. The NAPCR1 isolates were multidrug resistant (MDR) and commonly exhibited very high resistance levels. By sequencing their genomes, we showed that they possessed resistance-associated SNPs in gyrA and rpoB and carried eight to nine acquired antimicrobial resistance (AMR) genes. Most of these genes were located on known or novel mobile genetic elements shared by isolates recovered at different hospitals and at different time points. Metronidazole and vancomycin remain the first-line treatment options for these isolates. Overall, the NAPCR1 lineage showed an enhanced ability to acquire AMR genes through lateral gene transfer. On the basis of this finding, we recommend further vigilance and the adoption of improved control measures to limit the dissemination of this lineage and the emergence of more C. difficile MDR strains.

Signature of Microbial Dysbiosis in Periodontitis.

Periodontitis is driven by disproportionate host inflammatory immune responses induced by an imbalance in the composition of oral bacteria; this instigates microbial dysbiosis, along with failed resolution of the chronic destructive inflammation. The objectives of this study were to identify microbial signatures for health and chronic periodontitis at the genus level and to propose a model of dysbiosis, including the calculation of bacterial ratios. Published sequencing data obtained from several different studies (196 subgingival samples from patients with chronic periodontitis and 422 subgingival samples from healthy subjects) were pooled and subjected to a new microbiota analysis using the same Visualization and Analysis of Microbial Population Structures (VAMPS) pipeline, to identify microbiota specific to health and disease. Microbiota were visualized using CoNet and Cytoscape. Dysbiosis ratios, defined as the percentage of genera associated with disease relative to the percentage of genera associated with health, were calculated to distinguish disease from health. Correlations between the proposed dysbiosis ratio and the periodontal pocket depth were tested with a different set of data obtained from a recent study, to confirm the relevance of the ratio as a potential indicator of dysbiosis. Beta diversity showed significant clustering of periodontitis-associated microbiota, at the genus level, according to the clinical status and independent of the methods used. Specific genera (Veillonella, Neisseria, Rothia, Corynebacterium, and Actinomyces) were highly prevalent (>95%) in health, while other genera (Eubacterium, Campylobacter, Treponema, and Tannerella) were associated with chronic periodontitis. The calculation of dysbiosis ratios based on the relative abundance of the genera found in health versus periodontitis was tested. Nonperiodontitis samples were significantly identifiable by low ratios, compared to chronic periodontitis samples. When applied to a subgingival sample set with well-defined clinical data, the method showed a strong correlation between the dysbiosis ratio, as well as a simplified ratio (Porphyromonas, Treponema, and Tannerella to Rothia and Corynebacterium), and pocket depth. Microbial analysis of chronic periodontitis can be correlated with the pocket depth through specific signatures for microbial dysbiosis.IMPORTANCE Defining microbiota typical of oral health or chronic periodontitis is difficult. The evaluation of periodontal disease is currently based on probing of the periodontal pocket. However, the status of pockets "on the mend" or sulci at risk of periodontitis cannot be addressed solely through pocket depth measurements or current microbiological tests available for practitioners. Thus, a more specific microbiological measure of dysbiosis could help in future diagnoses of periodontitis. In this work, data from different studies were pooled, to improve the accuracy of the results. However, analysis of multiple species from different studies intensified the bacterial network and complicated the search for reproducible microbial signatures. Despite the use of different methods in each study, investigation of the microbiota at the genus level showed that some genera were prevalent (up to 95% of the samples) in health or disease, allowing the calculation of bacterial ratios (i.e., dysbiosis ratios). The correlation between the proposed ratios and the periodontal pocket depth was tested, which confirmed the link between dysbiosis ratios and the severity of the disease. The results of this work are promising, but longitudinal studies will be required to improve the ratios and to define the microbial signatures of the disease, which will allow monitoring of periodontal pocket recovery and, conceivably, determination of the potential risk of periodontitis among healthy patients.

Emergence of an outbreak-associated Clostridium difficile variant with increased virulence.

The prevalence of Clostridium difficile infections has increased due to the emergence of epidemic variants from diverse genetic lineages. Here we describe the emergence of a novel variant during an outbreak in a Costa Rican hospital that was associated with severe clinical presentations. This C. difficile variant elicited higher white blood cell counts and caused disease in younger patients than did other strains isolated during the outbreak. Furthermore, it had a recurrence rate, a 30-day attributable disease rate, and disease severity as great as those of the epidemic strain NAP1. Pulsed-field gel electrophoresis genotyping indicated that the outbreak strains belong to a previously undescribed variant, designated NAPCR1. Whole-genome sequencing and ribotyping indicated that the NAPCR1 variant belongs to C. difficile ribotype 012 and sequence type 54, as does the reference strain 630. NAPCR1 strains are resistant to fluoroquinolones due to a mutation in gyrA, and they possess an 18-bp deletion in tcdC that is characteristic of the epidemic, evolutionarily distinct, C. difficile NAP1 variant. NAPCR1 genomes contain 10% more predicted genes than strain 630, most of which are of hypothetical function and are present on phages and other mobile genetic elements. The increased virulence of NAPCR1 was confirmed by mortality rates in the hamster model and strong inflammatory responses induced by bacteria-free supernatants in the murine ligated loop model. However, NAPCR1 strains do not synthesize toxin A and toxin B at levels comparable to those in NAP1 strains. Our results suggest that the pathogenic potential of this emerging C. difficile variant is due to the acquisition of hypothetical functions associated with laterally acquired DNA.

In vivo animal models confirm an increased virulence potential and pathogenicity of the NAP1/RT027/ST01 genotype within the Clostridium difficile MLST Clade 2.

BACKGROUND: Based on MLST analyses the global population of C. difficile is distributed in eight clades, of which Clade 2 includes the "hypervirulent" NAP1/RT027/ST01 strain along with various unexplored sequence types (STs). METHODS: To clarify whether this clinically relevant phenotype is a widespread feature of C. difficile Clade 2, we used the murine ileal loop model to compare the in vivo pro-inflammatory (TNF-α, IL-1ß, IL-6) and oxidative stress activities (MPO) of five Clade 2 clinical C. difficile isolates from sequence types (STs) 01, 41, 67, and 252. Besides, we infected Golden Syrian hamsters with spores from these strains to determine their lethality, and obtain a histological evaluation of tissue damage, WBC counts, and serum injury biomarkers (LDH, ALT, AST, albumin, BUN, creatinine, Na+, and Cl-). Genomic distances were calculated using Mash and FastANI to explore whether the responses were dictated by phylogeny. RESULTS: The ST01 isolate tested ranked first in all assays, as it induced the highest overall levels of pro-inflammatory cytokines, MPO activity, epithelial damage, biochemical markers, and mortality measured in both animal models. Statistically indistinguishable or rather similar outputs were obtained for a ST67 isolate in tests such as tissue damage, neutrophils count, and lethal activity. The results recorded for the two ST41 isolates tested were of intermediate magnitude and the ST252 isolate displayed the lowest pathogenic potential in all animal experiments. This ordering matched the genomic distance of the ST01 isolate to the non-ST01 isolates. CONCLUSIONS: Despite their close phylogenic relatedness, our results demonstrate differences in pathogenicity and virulence levels in Clade 2 C. difficile strains, confirm the high severity of infections caused by the NAP1/RT027/ST01 strain, and highlight the importance of C. difficile typing.

Maternal Linoleic Acid Overconsumption Alters Offspring Gut and Adipose Tissue Homeostasis in Young but Not Older Adult Rats.

Maternal n-6 polyunsaturated fatty acids (PUFA) consumption during gestation and lactation can predispose offspring to the development of metabolic diseases such as obesity later in life. However, the mechanisms underlying the potential programming effect of n-6 PUFA upon offspring physiology are not yet all established. Herein, we investigated the effects of maternal and weaning linoleic acid (LA)-rich diet interactions on gut intestinal and adipose tissue physiology in young (3-month-old) and older (6-month-old) adult offspring. Pregnant rats were fed a control diet (2% LA) or an LA-rich diet (12% LA) during gestation and lactation. At weaning, offspring were either maintained on the maternal diet or fed the other diet for 3 or 6 months. At 3 months of age, the maternal LA-diet favored low-grade inflammation and greater adiposity, while at 6 months of age, offspring intestinal barrier function, adipose tissue physiology and hepatic conjugated linoleic acids were strongly influenced by the weaning diet. The maternal LA-diet impacted offspring cecal microbiota diversity and composition at 3 months of age, but had only few remnant effects upon cecal microbiota composition at 6 months of age. Our study suggests that perinatal exposure to high LA levels induces a differential metabolic response to weaning diet exposure in adult life. This programming effect of a maternal LA-diet may be related to the alteration of offspring gut microbiota.

The oral microbiota: a literature review for updating profesional s in dentistry-Part II / La microbiota oral: una revisión de literatura para la actualización de profesionales en odontología-Parte II

ABSTRACT: In the first part of this literature review, published in October 2019 in this journal, we summarized the conceptual background of the oral microbiota, and the main methods used in microbiology to characterize oral organisms. We also presented the most studied bacteria species in the oral microbiota. In this second part, we will discuss the evidence regarding the biological plausibility linking the oral microbiota dysbiosis and systemic diseases, as well as the main factors and mechanisms suspected in this association.

RESUMEN: En la primera parte de esta revisión de literatura, publicada en esta revista en octubre de 2019, se resumieron los antecedentes conceptuales de la microbiota oral y describieron los principales métodos utilizados en microbiología para caracterizar los microorganismos orales. Asimismo, se presentaron las especies bacterianas mejor estudiadas de la microbiota oral. En esta segunda parte, se explorará la plausibilidad biológica que vincularía la disbiosis de la microbiota oral y las enfermedades sistémicas, así como las características que podrían influenciar la composición de la microbiota oral.

Deletion of IQGAP1 promotes Helicobacter pylori-induced gastric dysplasia in mice and acquisition of cancer stem cell properties in vitro.

Helicobacter pylori infection is responsible for gastric carcinogenesis but host factors are also implicated. IQGAP1, a scaffolding protein of the adherens junctions interacting with E-cadherin, regulates cellular plasticity and proliferation. In mice, IQGAP1 deficiency leads to gastric hyperplasia. The aim of this study was to elucidate the consequences of IQGAP1 deletion on H. pylori-induced gastric carcinogenesis.Transgenic mice deleted for iqgap1 and WT littermates were infected with Helicobacter sp., and histopathological analyses of the gastric mucosa were performed. IQGAP1 and E-cadherin expression was evaluated in gastric tissues and in gastric epithelial cell lines in response to H. pylori infection. The consequences of IQGAP1 deletion on gastric epithelial cell behaviour and on the acquisition of cancer stem cell (CSC)-like properties were evaluated. After one year of infection, iqgap1+/- mice developed more preneoplastic lesions and up to 8 times more gastro-intestinal neoplasia (GIN) than WT littermates. H. pylori infection induced IQGAP1 and E-cadherin delocalization from cell-cell junctions. In vitro, knock-down of IQGAP1 favoured the acquisition of a mesenchymal phenotype and CSC-like properties induced by H. pylori infection.Our results indicate that alterations in IQGAP1 signalling promote the emergence of CSCs and gastric adenocarcinoma development in the context of an H. pylori infection.

The Oral Microbiota: A Literature Review for Updating Professionals in Dentistry. Part I / La microbiota oral: una revisión de literatura para la actualización de profesionales en odontología. Parte I

Abstract In recent decades, a body of literature examining the relationships between oral health and general health has rapidly developed. However, the biological mechanisms involved in explaining such relationships have not been fully described. Recent evidence has suggested that these relationships could be partially explained by the composition and interaction of the microbiome/microbiota between local and systemic body sites. For instance, it has been suggested that intestinal microbiota could have effects on non-communicable diseases, such as diabetes or cardiovascular diseases. The objective of this study is to explore current evidence of the link between oral and systemic diseases, to discuss whether oral microbiome/microbiota could represent an unexplored biological pathway partially explaining those relationships. A non-systematic review of the literature was carried out using keyword searches in Pubmed from February to May 2019. The ultimate goal was to present recent scientific evidence to update the general knowledge on this topic to professionals in dentistry. This review is divided in two parts for journal publication; however, it is intended to be used as one piece. In this first part, we will summarize the conceptual background of oral microbiome/microbiota, we will describe the main methods used in microbiology to characterize oral organisms, and will present the main composition of bacteria in oral microbiome/microbiota. The second part highlights the main evidence regarding the biological plausibility that links oral microbiome and systemic diseases and we will conclude with some future research recommendations. Taking into account the role of oral microbiota in the development of systemic diseases could change the main paradigm of how oral health is currently conceptualized by dental professionals.

Resumen En las últimas décadas, se ha acumulado evidencia sobre las relaciones existentes entre la salud oral y la salud general. Sin embargo, los mecanismos biológicos implicados en la explicación de tales relaciones no se han logrado describir completamente. Investigaciones recientes han sugerido que parte de esta relación se podría explicar por la composición e interacción del microbioma o la microbiota a nivel local y sistémico. Por ejemplo, la evidencia ha mostrado que la microbiota intestinal parece tener efectos sobre enfermedades crónicas no transmisibles, como la diabetes o las enfermedades cardiovaculares. En esta revisión bibliográfica, se han seleccionado algunos estudios que han tratado de hipotetizar que el microbioma y la microbiota oral podrían representar un mecanismo biológico poco explorado que podría explicar parcialmente las relaciones que se han observado entre condiciones orales y enfermedades sistémicas. El objetivo de esta revisión es analizar la evidencia actual que explica los posibles mecanismos que desempeñan un papel en las asociaciones entre la salud oral y la salud sistémica. La hipótesis discutida es que el microbioma y microbiota oral podría ser un mecanismo biológico que podría explicar parcialmente las influencias de las enfermedades orales sobre la salud general. Se realizó una revisión no sistemática de la literatura entre febrero y mayo del 2019 en la plataforma PubMed. El objetivo final es presentar evidencia científica reciente para actualizar el conocimiento general sobre este tema para los profesionales en odontología. Esta revisión se presenta en dos partes por consideraciones editoriales, sin embargo, la intención es que ambas sean leídas como una sola pieza. En esta primera parte, se presentarán las bases conceptuales, se describirán los principales métodos utilizados en microbiología para caracterizar los organismos orales y se mencionará la composición descrita en la literatura de los principales microorganismos presentes en la microbiota oral. En la segunda parte, se sintetizará la evidencia principal sobre la plausibilidad biológica que vincula el microbioma oral y las enfermedades sistémicas, y concluiremos con algunas recomendaciones de investigación futuras. Esta perspectiva podría cambiar el paradigma principal de cómo se conceptualiza actualmente la salud oral por parte de los profesionales en odontología.

Evidencias clínicas del uso de moduladores de la microbiota intestinal para el tratamiento de trastornos mentales: una revisión bibliográfica sistemática / Clinical evidence about the use of gut microbiota modulators as treatment for mental health disorders: A systematic review

Existe una asociación entre la disbiosis intestinal, el eje intestino-cerebro y la salud mental. Empleando las bases de datos PubMed, Embase y Web of Science se realizó una revisión sistemática para analizar ensayos clínicos que evalúen el uso de moduladores de la microbiota intestinal en el tratamiento de trastornos mentales. La calidad metodológica de los estudios encontrados se evaluó utilizando la guía CONSORT. Únicamente 8 artículos fueron aptos para el análisis propuesto: 5 correspondían a pacientes con depresión y únicamente uno correspondía ya fuera a esquizofrenia, trastorno por déficit de atención e hiperactividad o Alzheimer. Es posible concluir que los moduladores de la microbiota pueden ser una terapia coadyuvante efectiva junto a los medicamentos antidepresivos y antipsicóticos tradicionales. La heterogeneidad de las intervenciones, el pequeño tamaño de la muestra, la falta de evaluación de la microbiota intestinal y el autorreporte de síntomas son limitantes que deben solventarse antes de concluir. Número de registro PROSPERO: CRD42020202938. (AU)

There is an association between intestinal dysbiosis, the gut–brain axis and mental health. PubMed, Embase and Web of Science were searched for analysing clinical trials in which microbiota modulators are used in mental health disorders for this systematic review. An evaluation of each study was made using CONSORT and only eight articles were suitable for this analysis: five were in depressive patients, and only one corresponded to either schizophrenia, attention-deficit/hyperactivity disorder or Alzheimer's disease. It is possible to conclude that microbiota modulators might be effective coadjuvants in traditional antidepressant or antipsychotic drugs treatment. However, the heterogeneity of interventions, small sample size, lack of intestinal microbiota assessment and symptoms auto report should be addressed before a conclusion can be made. PROSPERO registration number: CRD42020202938. (AU)